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Pathseq pipeline fatal error

We are trying to run the Path-seq pipeline (PathSeqPipelineSpark) using a bam that contains bulk RNA-seq reads we extracted from a human sample but do not map to the human genome. We are hoping to find out what these reads might be. We have downloaded the tutorial and it runs great. We are using all of the files from the ftp path for the microbe fasta & img, host img, and taxonomy files. All of our options are identical to those given in the tutorial. We are running into a "fatal error detected by the Java Runtime Environment." It seems to be occurring in stage 21. It also says the crash happened outside the Java Virtual Machine in native code. We have allocated ample memory for the pipeline so we don't think memory is causing the issue. Are there any ideas as to what we could do to get around this error?
Much thanks!

Answers

  • markwmarkw admin Cambridge, MAMember, Broadie, Moderator, Dev admin

    Hello @biff

    What environment are you running in? Also, can you please post the command you used to launch the tool?

  • Hi

    I'm having the exact same error - I'm running this on a Ubuntu image running on our local cloud system. Trying to analyse a human WGS file (~200GB). I've allocated 128GB memory but it crashes out at this stage. The command I'm using is:

    _gatk PathSeqPipelineSpark --input DNA_A01.bam --filter-bwa-image pathseq_host.fa.img --kmer-file pathseq_host.hss --min-clipped-read-length 70 --microbe-fasta pathseq_microbe.fa --microbe-bwa-image pathseq_microbe.fa.img --taxonomy-file microbe.db --output LP.pathseq.bam --scores-output LP.pathseq.txt --java-options "-Xmx128G"
    _

    18/08/06 10:09:57 INFO Executor: Running task 14.0 in stage 21.0 (TID 38570)
    18/08/06 10:09:57 INFO Executor: Running task 9.0 in stage 21.0 (TID 38565)
    18/08/06 10:09:57 INFO Executor: Running task 8.0 in stage 21.0 (TID 38564)
    18/08/06 10:09:57 INFO Executor: Running task 7.0 in stage 21.0 (TID 38563)
    18/08/06 10:09:57 INFO Executor: Running task 4.0 in stage 21.0 (TID 38560)
    18/08/06 10:09:57 INFO Executor: Running task 10.0 in stage 21.0 (TID 38566)
    #

    A fatal error has been detected by the Java Runtime Environment:

    #

    SIGSEGV (0xb) at pc=0x00007fcc6aac62cc, pid=1503, tid=0x00007fcc70ae2700

    #

    JRE version: OpenJDK Runtime Environment (8.0_171-b11) (build 1.8.0_171-8u171-b11-0ubuntu0.16.04.1-b11)

    Java VM: OpenJDK 64-Bit Server VM (25.171-b11 mixed mode linux-amd64 )

    Problematic frame:

    C [libbwa.5405576633662980144.jnilib+0x92cc] bwa_mem2idx+0xcc

    I've attached an error log too.

  • markwmarkw admin Cambridge, MAMember, Broadie, Moderator, Dev admin

    Hello @adbeggs

    Can you try running this again with 200GB memory? 128GB may be too little.

  • I had exactly the same error, and it turned out that my image file was truncated during a transfer. Be sure that all of your image/reference files are the sizes they should be

  • So I solved that problem - as Tom_L quite rightly says it is a truncated image file. My main issue now is speed - it has been running now on a 256gb VM for 9 days....
    The latest messages are:

    /08/20 14:05:12 INFO ShuffleBlockFetcherIterator: Started 0 remote fetches in 0 ms
    18/08/20 14:22:30 INFO BlockManagerInfo: Removed broadcast_1_piece0 on 172.31.9.59:39737 in memory (size: 9.5 KB, free: 68.0 GB)
    18/08/20 14:22:30 INFO BlockManagerInfo: Removed broadcast_2_piece0 on 172.31.9.59:39737 in memory (size: 2.9 KB, free: 68.0 GB)
    18/08/20 14:22:30 INFO BlockManagerInfo: Removed broadcast_16_piece0 on 172.31.9.59:39737 in memory (size: 3.0 KB, free: 68.0 GB)

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